MacroModel Reference Manual - ISP

ContentsDocument Conventions .................................................................................................... viiChapter 1: Capabilities and New Features........................................................... 11.1 General Description .................................................................................................. 11.2 Energetic Calculations ............................................................................................. 11.2.1 Force Fields and Energy Equations.................................................................... 11.2.2 Energy Minimization Methods............................................................................. 41.2.3 Conformational Searching and Comparison ....................................................... 51.2.4 Molecular Dynamics and Monte Carlo Simulations ............................................ 61.2.5 Coordinate Manipulation ..................................................................................... 61.2.6 Molecular Association ......................................................................................... 61.2.7 Partition Coefficients ........................................................................................... 71.2.8 Free-energy Perturbation .................................................................................... 71.2.9 Monte Carlo Simulation....................................................................................... 71.3 Computational Features........................................................................................... 71.4 Program Capacity...................................................................................................... 91.5 Miscellaneous ............................................................................................................ 91.6 Citing MacroModel in Publications ........................................................................ 9Chapter 2: Running MacroModel .............................................................................. 112.1 Running MacroModel From the Command Line................................................ 112.1.1 Environment Variables ...................................................................................... 112.1.2 Command-line Syntax....................................................................................... 122.1.3 Storage of Temporary Files............................................................................... 132.1.4 The .com File .................................................................................................... 142.1.4.1 File Specifications.................................................................................. 142.1.4.2 Operation Code Specifications ............................................................... 152.1.4.3 Using an Executable .com File................................................................ 162.2 Job Control............................................................................................................... 172.2.1 Interacting With a Running MacroModel Job Via Files ..................................... 172.2.1.1 Stopping MacroModel ............................................................................ 18MacroModel 9.7 Reference Manualiii